GOTreePlus consists of two lists (GO term list and gene list) on the left and TreePlus on the right
Select the source file and annotation file using "Open..." buttons in the "OpenFiles" dialog.
"Mapping field" is the field in the annotation file to which the first column in the source file is mapped.
There are two fields that can be used as a mapping field: 1) DB_Object_ID (e.g. UniProt ID) and 2) DB_Object_Symbol (e.g. UniProt Symbol).
Default mapping filed is DB_Object_Symbol.
GO Annotation files are available at the Gene Ontology website.
Source File Format
- First two lines will be ignored. The first line can be a description of the dataset. The second line has column headers.
- As shown below, the first column should be an id, the second should be a value, and the third should be a name.
Download this sample input file
Annotation File Format
Gene Ontology annotation files are tab-delimited text files, which follows the GO annotation file format guide.
- Any line starts with '!' will be ignored.
- As shown below, the second column should be "DB_Object_ID" (e.g. UniProt ID) and the third column should be "DB_Object_Symbol" (e.g. UnitProt Symbol).
- The ninth column should be the character code to represent a name space; 'C' for Cellular Component, 'F' for Molecular Function, and 'P' for Biological Process.
Download this annotation file for the sample input file
or go to GO Annotations page and select the annotation file for "Homo sapiens."
Similarly, users can also search proteins/genes by id or name (e.g., "placental growth factor") given in the input source file. Labels in the proteins/genes list are grayed out if there is no GO term associated with the item in the current name space. When users select an item from the proteins/genes list, all GO terms related to the selected item are shown in the gene ontology structure in TreePlus. If the "Proteins/Genes" radio button is selected, the GO term list is updated with the GO terms associated with the selected proteins/genes. The number of GO terms in the list is also updated and shown by the "GO Terms" radio button.
Name Space
Since three name spaces "Biological Process, Cellular Component, and Molecular Function" are disjoint from each other, GOTreePlus visualizes one name space at a time. Users can select one name space among the three using the combo box above the GO term list. The search for GO terms is performed within the selected name space.
Categorize by
Users can choose either "Own Annotation" (average value of the proteins mapped to a node) or "Total Annotation" (average value of the proteins mapped to a node or its descendants) to color the circular dot in GO nodes.
Count Only
When users want to see how only "up-regulated" proteins are mapped to GO, users can select "Up" in this combobox. When they are interested in only the "down-regulated" proteins, they can choose "Down" in the combobox. "All" is the default value with which GOTreePlus uses all proteins regardless of up/down regulation.
Order By
Users can order child nodes of a GO node according to "Own Annotation" (number of its own annotation) or "Total Annotation" (sum of its descendants' and its own annotation).
Home
Users can reset the TreeControl to the initial view where the top-level node of the current ontology is open.
Hide Legend
Users can hide the legend to see only the GO structure in the TreePlus control.
Fit in Window
The TreePlus control scales the current GO display to show all open nodes within the GOTreePlus control.
Default Size
This resets the zoom-level to the initial level.
Zoom
Users can zoom in or out by dragging the slider bar. Users can pan the GO structure display as well by dragging the canvas.
- Set as Root
Unlike other GO browsers, GOTreePlus enables users to select any GO term and make it the root node to initiate a focused exploration from the node.
- Retrieve annotated proteins/genes
Users can also populate the proteins/genes list with the proteins/genes mapped to the selected GO node. - Export annotated proteins/genes (only this node)
Users can save the proteins/genes mapped to the selected node in a text file. - Export annotated proteins/genes (this node & below)
Users can save the proteins/genes mapped to the selected node or its descendants in a text file. - Show annotation distribution
Users can select any node to see a localized overview of annotation distribution over its children nodes in a standard pie chart with a coordinated list view.
The pie chart is coordinated with the list control below and the TreePlus control. When users mouse over on a slice at the pie chart, the corresponding item on the list and the corresponding node on the TreePlus control will be highlighted. When users select an item on the list control, the corresponding parts in the pie chart and the TreePlus control are highlighted.